TPP:4.5.0 Release Notes

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Trans-Proteomic Pipeline (TPP) "<name>" 4.5.0 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. The software is available for Windows as well as linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a webserver). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.4.1_Release_Notes

Contents

[edit]

New Features/Changes

  • TBD
[edit]

Bug fixes and improvements

  • TBD
[edit]

Known Issues

  • None to report
[edit]

Getting the TPP Software

  • Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_name?_rev_1.exe) from the Sashimi SourceForge project file release page: 
 "http://sourceforge.net/projects/sashimi/files/"
  • Everyone is encouraged to read and contribute to our wiki, at 
 "http://tools.proteomecenter.org/wiki/"
  • For guides to installing and using our software, please see our wiki: 
 "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"
  • For downloading the source code, please go to the following link: 
 "http://sourceforge.net/projects/sashimi/files/" and find the 4.4.1 source code .zip package;

or, check out the code directly from svn: 

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-1"

 For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Brian, Natalie, and Joe plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

== SVN Log

r5401 | mhoopmann | 2011-05-20 09:32:40 -0700 (Fri, 20 May 2011) | 1 line

Added another function from RAMP.

r5400 | dshteyn | 2011-05-18 15:10:36 -0700 (Wed, 18 May 2011) | 1 line

InterProphetParser: BUGFIX, correct the outputting of extra </spectrum_query> tags.

r5399 | slagelwa | 2011-05-18 11:25:26 -0700 (Wed, 18 May 2011) | 3 lines

Adding a snapshot of the new TPP Web Launcher for Amazon so I don't lose anything.


r5398 | slagelwa | 2011-05-16 10:54:02 -0700 (Mon, 16 May 2011) | 1 line

[4.5 branch] creating branch from trunk. Code for all 4.5.x releases lives here

r5397 | slagelwa | 2011-05-13 16:57:14 -0700 (Fri, 13 May 2011) | 11 lines

  • Decreased the minimum time between checks for results. The 
 window was still large enough for eventual consistency 
 problems.
  • Incl. ability to set max sleep time on poll
  • Yet another fix to the fork/zombie issue in the client.

Now properly handles them by reaping them and *not* ignoring the children processes.


r5396 | mhoopmann | 2011-05-12 17:12:12 -0700 (Thu, 12 May 2011) | 1 line

Workaround added for Mascot2XML. It was far easier to add an exception here than to fix that code.

r5395 | slagelwa | 2011-05-12 14:14:14 -0700 (Thu, 12 May 2011) | 11 lines

  • Burned yet again by eventual consistency. Race condition

existed where queues *looked* empty but werent and the client shutdown. Reworked main loop so that it'll poll for 5 mins before quitting.

  • Corrected signal processing issue with zombies. Similar

issue existed in forked system() calls in the download

  • Lastly, client process not quitting on signal properly


r5394 | eng_jk | 2011-05-11 17:40:19 -0700 (Wed, 11 May 2011) | 4 lines

Modifications to allow xpress to work with input mzML files with non-sequential native scanId numbers. Only the core XPressPeptideParser.exe has been updated; there's no good way for the cgi gui chromatogram interface to support these data files.

r5393 | pcbrefugee | 2011-05-11 11:36:08 -0700 (Wed, 11 May 2011) | 1 line

[pwiz] synch up with official code rev 2689

r5392 | slagelwa | 2011-05-10 11:58:41 -0700 (Tue, 10 May 2011) | 3 lines

Report wall time of search use different format for pid filename

r5391 | pcbrefugee | 2011-05-03 15:51:11 -0700 (Tue, 03 May 2011) | 1 line

[xtandem for hadoop and mpi] a few object serialization tweaks for "refine" step support

r5390 | eng_jk | 2011-05-03 13:36:33 -0700 (Tue, 03 May 2011) | 2 lines

minor mods to increase precision of mass tol in xpress chromatogram gui; replace hydrogen mass with proton mass in code

r5389 | mhoopmann | 2011-05-03 11:31:54 -0700 (Tue, 03 May 2011) | 1 line

Added scanIndex data member to BasicSpectrum and RAMP interface to provide sequential scan numbering independent of numbers used by instrument manufacturers.

r5388 | eng_jk | 2011-05-02 10:52:17 -0700 (Mon, 02 May 2011) | 2 lines

add -static-libstdc++ compiler flag

r5387 | eng_jk | 2011-04-27 16:26:56 -0700 (Wed, 27 Apr 2011) | 2 lines

Add command line option -M to allow user to specify static mods

r5386 | mhoopmann | 2011-04-27 09:38:29 -0700 (Wed, 27 Apr 2011) | 1 line

Fixed missing last scan indexing bug when using spectra without scan numbers. Also suppressed warning messages that appear when spectra do not have scan numbers.

r5385 | mhoopmann | 2011-04-26 15:35:26 -0700 (Tue, 26 Apr 2011) | 1 line

Ack! Cleaning up test output to screen that was left in at last check-in.

r5384 | mhoopmann | 2011-04-26 15:32:55 -0700 (Tue, 26 Apr 2011) | 1 line

Force spectrum object to use index number when spectrum has no scan number (for cramp functionality).

r5383 | mhoopmann | 2011-04-25 13:44:35 -0700 (Mon, 25 Apr 2011) | 1 line

Default precursor scan number to 0 when not provided.

r5382 | dshteyn | 2011-04-25 11:14:51 -0700 (Mon, 25 Apr 2011) | 1 line

Undo Makefile change that broke linux build. And change mzParser to respond to -D__LINUX__ as to -DGCC.

r5381 | pcbrefugee | 2011-04-20 17:06:42 -0700 (Wed, 20 Apr 2011) | 1 line

tweak for building with mingw

r5380 | pcbrefugee | 2011-04-20 17:05:58 -0700 (Wed, 20 Apr 2011) | 1 line

avoid redefine of XML_STATIC for quiet compile

r5379 | dshteyn | 2011-04-20 11:55:34 -0700 (Wed, 20 Apr 2011) | 1 line

Tweaks to compilation on Linux.

r5378 | dshteyn | 2011-04-20 11:11:29 -0700 (Wed, 20 Apr 2011) | 1 line

switch to zlib v1.2.5 and tweaks fro MingW build

r5377 | dshteyn | 2011-04-20 11:10:24 -0700 (Wed, 20 Apr 2011) | 1 line

update location of msconvert.exe

r5376 | dshteyn | 2011-04-20 11:09:21 -0700 (Wed, 20 Apr 2011) | 1 line

update zlib version to 1.2.5

r5375 | dshteyn | 2011-04-20 11:00:47 -0700 (Wed, 20 Apr 2011) | 1 line

switching to zlib 1.2.5

r5374 | dshteyn | 2011-04-20 10:05:13 -0700 (Wed, 20 Apr 2011) | 1 line

MingW compilation tweaks

r5373 | dshteyn | 2011-04-19 16:42:07 -0700 (Tue, 19 Apr 2011) | 1 line

Mingw compilation

r5372 | dshteyn | 2011-04-19 16:41:03 -0700 (Tue, 19 Apr 2011) | 1 line

Mingw compilation

r5371 | dshteyn | 2011-04-19 15:49:46 -0700 (Tue, 19 Apr 2011) | 1 line

InteractParser: option for recording the retention_time_sec in pepXML.

r5370 | slagelwa | 2011-04-19 15:11:12 -0700 (Tue, 19 Apr 2011) | 10 lines

  • Corrected issue with SIGCHLD on server process. system() call was 
 returning "No child processes" error when started through cloud-init.  No
 longer set the sig handler to ignore
  • Fixed some issues with inspect, primarily setting of the database to 
 search against
  • Better error checking in client responses
  • Fixed typo
  • Added amzbill to fetch the latest billing reports. Script not installed 
 but just part of the distro

r5369 | slagelwa | 2011-04-15 16:16:19 -0700 (Fri, 15 Apr 2011) | 13 lines

  • added reporting back into the program 
  * requeues download msg in order to pass back download
    information to parent process for reporting
  • amztpp no longer creates the SQS queues every time it runs
  • clean no longer shuts down the nodes (use terminate to 
 accomplish this)
  • added back shutting down ec2 instance when server process 
 ends
  • debug print # visible and not visible messages in queues
  • always query for ec2 instances
  • others...


r5368 | mhoopmann | 2011-04-14 12:21:48 -0700 (Thu, 14 Apr 2011) | 1 line

Fixed a bug that prevented spectra with a scan number of 0 from being read.

r5367 | dshteyn | 2011-04-14 11:19:02 -0700 (Thu, 14 Apr 2011) | 1 line

BUGFIX: Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.

r5366 | dshteyn | 2011-04-13 09:31:32 -0700 (Wed, 13 Apr 2011) | 1 line

InterProphetParser: BUGFIX When the pepXML already contains the iProphet tags filter them out, including the end tag.

r5365 | pcbrefugee | 2011-04-12 17:30:06 -0700 (Tue, 12 Apr 2011) | 1 line

set line ending to unix style (helps when running VMWare hosted linux sharing a windows source code directory)

r5364 | pcbrefugee | 2011-04-12 16:55:16 -0700 (Tue, 12 Apr 2011) | 1 line

[mr-tandem] better logging and fixes for refinement step in mapreduce xtandem

r5363 | slagelwa | 2011-04-06 22:45:58 -0700 (Wed, 06 Apr 2011) | 16 lines

  • Additional updates to the documentation
  • Info messages are now outputted to console (in non-debug format) 
 they also now have a rudimentary formatting capability.  (Maybe one
 of these days change it over to Log::Log4perl)
  • Version string is now taken out of AWS.pm 
  * also added -V to server program
  • Fixed die message logging in server/client
  • Removed Proc::Fork dependence
  • Added info messages in clean command
  • Group (AMZTPP) used for instance detection
  • Looks for AMI's using new naming nomenclature
  • Shutdown added to server on process exit
  • Added back the autostarting of instances
  • Others...


r5362 | pcbrefugee | 2011-03-31 15:48:50 -0700 (Thu, 31 Mar 2011) | 1 line

[hadoop xtandem] move launcher scripts over to the Insilicos Cloud Army project where the X!!Tandem (MPI xtandem) support scripts already live. Change the readme-mapreduce to point users to https://ica.svn.sourceforge.net/svnroot/ica/

r5361 | slagelwa | 2011-03-30 17:23:44 -0700 (Wed, 30 Mar 2011) | 22 lines

Major revision of the TPP Amazon Cloud stuff 2.0 Alpha

Changes include: 

  * New command line interface, merged scripts into one client program
  * Updated documentation
  * Explict controls over background process
  * Client can do parallel upload/downloads in background
  * Support for Myrimatch
  * Uses new CloudInit boot in images
  * Uses new TPP Amazon image based on Ubuntu 10.x
  * Now creates a Amazon default security group (named SPCTools-TPP)
    if one not specified
  * Now loads Moose related modules *AFTER* processing arguments
  * Fixed issue with starting too many nodes at the beginning
  * Directory "Search" removed from packages
  * Configurable sandbox area on server
  * Server program renamed
  * Better/detailed querying of queued messages


r5360 | dshteyn | 2011-03-28 12:18:09 -0700 (Mon, 28 Mar 2011) | 1 line

GCC: anonymous struct warning.

r5359 | dshteyn | 2011-03-25 16:31:27 -0700 (Fri, 25 Mar 2011) | 1 line

Makefile.incl was not checked in

r5358 | dshteyn | 2011-03-25 16:00:08 -0700 (Fri, 25 Mar 2011) | 1 line

InteractParser: SearchHit Changes, also defines bool_hash used in RTCatalog.

r5357 | dshteyn | 2011-03-25 15:35:21 -0700 (Fri, 25 Mar 2011) | 1 line

Makefile changes to get all this to compile with new code and mzParser.

r5356 | dshteyn | 2011-03-25 15:33:40 -0700 (Fri, 25 Mar 2011) | 1 line

PTMProphetParser: first commit

r5355 | dshteyn | 2011-03-25 15:24:50 -0700 (Fri, 25 Mar 2011) | 1 line

ramp -> mzParser switch

r5354 | dshteyn | 2011-03-25 15:15:09 -0700 (Fri, 25 Mar 2011) | 1 line

SpectraST: Allow SpectraST to compile as lib only (no main) function so it can be used in other tools. Also ramp ->mzParser changes.

r5353 | dshteyn | 2011-03-25 15:05:31 -0700 (Fri, 25 Mar 2011) | 1 line

switch ramp -> mzParser

r5352 | dshteyn | 2011-03-25 14:55:53 -0700 (Fri, 25 Mar 2011) | 1 line

switch ramp -> mzParser

r5351 | dshteyn | 2011-03-25 14:45:42 -0700 (Fri, 25 Mar 2011) | 1 line

XPress: switch ramp -> mzParser.

r5350 | dshteyn | 2011-03-25 14:42:28 -0700 (Fri, 25 Mar 2011) | 1 line

ASAPRatio: switch ramp -> mzParser, add options to quantify only above certain probability.

r5349 | dshteyn | 2011-03-25 14:13:14 -0700 (Fri, 25 Mar 2011) | 1 line

ramp -> mzParser switch.

r5348 | mhoopmann | 2011-03-25 12:19:23 -0700 (Fri, 25 Mar 2011) | 1 line

more legacy support

r5347 | dshteyn | 2011-03-25 10:26:36 -0700 (Fri, 25 Mar 2011) | 1 line

Search2pepXML: converted to using mzParser instead of ramp.

r5346 | dshteyn | 2011-03-25 10:25:00 -0700 (Fri, 25 Mar 2011) | 1 line

PeptideProphetParser: tweak pI model to model only +-5 stdev from mean pI for run.

r5345 | dshteyn | 2011-03-25 10:23:34 -0700 (Fri, 25 Mar 2011) | 1 line

RTCatalogParser: tool for cataloging RTs

r5344 | dshteyn | 2011-03-25 10:10:34 -0700 (Fri, 25 Mar 2011) | 1 line

Pep3D: ramp -> mzParser switch.

r5343 | dshteyn | 2011-03-25 10:09:10 -0700 (Fri, 25 Mar 2011) | 1 line

PepXMLViewer: Update index to use longs to allow opening larger files. PTMProphetParser support. mzParser compatibility.

r5342 | dshteyn | 2011-03-25 10:04:22 -0700 (Fri, 25 Mar 2011) | 1 line

InteractParser: Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.

r5341 | dshteyn | 2011-03-25 10:03:54 -0700 (Fri, 25 Mar 2011) | 1 line

InteractParser: Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.

r5340 | pcbrefugee | 2011-03-24 14:34:35 -0700 (Thu, 24 Mar 2011) | 1 line

[windows installer] tweaks to handle gnuplot update in SVN ref 5124

r5339 | mhoopmann | 2011-03-24 11:04:38 -0700 (Thu, 24 Mar 2011) | 1 line

expanding more ramp functions

r5338 | henryhlam | 2011-03-24 00:15:45 -0700 (Thu, 24 Mar 2011) | 1 line

[SpectraST] Option to output library in PAIdent format for import into PeptideAtlas

r5337 | pcbrefugee | 2011-03-23 14:34:02 -0700 (Wed, 23 Mar 2011) | 4 lines

[Makefiles] finer-grained $ARCH detection for cross compiling with shared source tree, so one can build side by side mingw, Ubuntu, Centos, 32 and 64 bit versions, all on the same PC under VMWare using a single copy of the source in a shared mount. Also switches MinGW boost version to 1_45_0. This will be a long build the first time you use it.

r5336 | pcbrefugee | 2011-03-22 15:48:16 -0700 (Tue, 22 Mar 2011) | 1 line

[Makefile] some GCCs don't like trailing slash in -I include declarations

r5335 | henryhlam | 2011-03-17 21:03:53 -0700 (Thu, 17 Mar 2011) | 1 line

[SpectraST] Bracketing, Bayesian denoising (beta), option to not normalize, report TotalIonCurrent/PrecursorIntensity/OrigMaxIntensity of consensus as average of replicates rather than values of the best replicate

r5334 | henryhlam | 2011-03-17 20:59:05 -0700 (Thu, 17 Mar 2011) | 1 line

[SpectraST] Treat HCD as CID, and ETD-SA as ETD in peak annotation

r5333 | henryhlam | 2011-03-17 20:53:18 -0700 (Thu, 17 Mar 2011) | 1 line

[SpectraST] Display Xrea (quality measure) in Lib2HTML verbose mode

r5332 | mhoopmann | 2011-03-15 16:13:37 -0700 (Tue, 15 Mar 2011) | 1 line

Fixed bugs relating to k-score crashes. Crashes no longer occur on Windows. However, k-score results are not exactly replicated when compared to older versions. This may be intentional by the xtandem authors, however, we should identify what is causing such changes and decide if they are appropriate for k-score.

r5331 | dshteyn | 2011-03-09 12:50:21 -0800 (Wed, 09 Mar 2011) | 1 line

Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)

r5330 | mhoopmann | 2011-03-09 10:20:53 -0800 (Wed, 09 Mar 2011) | 1 line

Added cached RAMP support.

r5329 | dshteyn | 2011-03-09 09:55:21 -0800 (Wed, 09 Mar 2011) | 1 line

mzParser: access was already defined in a unix header, renamed to gz_access

r5328 | mhoopmann | 2011-03-08 15:48:48 -0800 (Tue, 08 Mar 2011) | 3 lines

Added support for .mzXML.gz and .mzML.gz files. These are slow for the first scan read as the inflation table is built. After that the overhead is minor.

Other changes are modest increases in file reading efficiency when performing scan by scan parsing.

r5327 | mhoopmann | 2011-03-07 16:50:17 -0800 (Mon, 07 Mar 2011) | 1 line

Bugfix

r5326 | mhoopmann | 2011-03-07 16:09:21 -0800 (Mon, 07 Mar 2011) | 1 line

Implemented readRunHeader for RAMP compatibility.

r5325 | dshteyn | 2011-03-07 15:10:08 -0800 (Mon, 07 Mar 2011) | 1 line

Adding FAIMS CompensationVoltage to mzParser.

r5324 | mhoopmann | 2011-03-03 08:57:34 -0800 (Thu, 03 Mar 2011) | 1 line

Expanding the parser to capture more metadata

r5323 | pcbrefugee | 2011-03-02 13:07:11 -0800 (Wed, 02 Mar 2011) | 1 line

[non-windows "make install"] don't try to install optional-build Pepc components if they aren't built

r5322 | real_procopio | 2011-03-01 15:41:14 -0800 (Tue, 01 Mar 2011) | 1 line

[plot-msms] Fix typo in var name when no ms1 peaks present

r5321 | dshteyn | 2011-03-01 12:18:45 -0800 (Tue, 01 Mar 2011) | 1 line

plot-msms-js.cgi: Look for lorikeet.css in DEFAULT_HTML_DIR/css not webroot/css

r5320 | slagelwa | 2011-02-25 16:00:54 -0800 (Fri, 25 Feb 2011) | 2 lines

Checking in first stab at a new Regis specific sequest script

r5319 | slagelwa | 2011-02-25 16:00:18 -0800 (Fri, 25 Feb 2011) | 3 lines

Now specifies the name of the spectrast log file, since it'll always write one anyhow.

r5318 | slagelwa | 2011-02-25 15:27:31 -0800 (Fri, 25 Feb 2011) | 2 lines

Wasn't logging, missing space in the command line creation

r5317 | slagelwa | 2011-02-25 15:26:51 -0800 (Fri, 25 Feb 2011) | 5 lines

  • Fixed issue with mascot using different results links
  • Now reports an error when no results link returned by mascot.

It turns out that some searches return incomplete without a results link but with a 200 OK. Presumbably its timing out on the web server side.

r5316 | mhoopmann | 2011-02-25 12:41:43 -0800 (Fri, 25 Feb 2011) | 1 line

Updated all our plugins so that they behave as prior to cyclone. There should be no compilation errors, and no halting when running tandem.

r5315 | mhoopmann | 2011-02-25 11:00:45 -0800 (Fri, 25 Feb 2011) | 1 line

cleaning up unused file

r5314 | mhoopmann | 2011-02-25 11:00:07 -0800 (Fri, 25 Feb 2011) | 1 line

Fixed bug when parsing empty spectra in mzXML files using RAMP interface.

r5313 | dshteyn | 2011-02-23 11:58:02 -0800 (Wed, 23 Feb 2011) | 1 line

InteractParser: bug fix associated with parsing OMSSA data.

r5312 | mhoopmann | 2011-02-23 09:58:24 -0800 (Wed, 23 Feb 2011) | 1 line

Fixed bug when handling uncompressed mzXML data

r5311 | dshteyn | 2011-02-18 17:47:28 -0800 (Fri, 18 Feb 2011) | 1 line

InteractParser: -P flag for OMSSA didn't fix the protein names for alternative_protein entries until this fix.

r5310 | dshteyn | 2011-02-16 10:53:23 -0800 (Wed, 16 Feb 2011) | 1 line

XPressPeptideParser: Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search

r5309 | slagelwa | 2011-02-16 10:34:22 -0800 (Wed, 16 Feb 2011) | 4 lines

By default set the umask of the job (and log files) to allow group access so that I can debug things when they go wrong.


r5308 | dshteyn | 2011-02-15 11:26:46 -0800 (Tue, 15 Feb 2011) | 1 line

ASAPRatioProteinCGIDisplay: use central code for parsing search results to avoid error when parsing new search engine.

r5307 | slagelwa | 2011-02-14 16:03:54 -0800 (Mon, 14 Feb 2011) | 8 lines

  • Fixed issue with SPECTRAST variable override not being used
  • Set default name for jobs
  • Fixed major issue with creating libraries. Now looks for the "-cN" flag 
 to spectrast and names the qjob and qlog files using this string.  In the
 past it ended up creating hidden files named .spectrast.qjob and
 .spectrast.qlog


r5306 | mhoopmann | 2011-02-14 12:31:20 -0800 (Mon, 14 Feb 2011) | 1 line

Added additional scoring plugins and dealt with PLUGGABLE_SCORING flag in add_A function of mscore.cpp.

r5305 | mhoopmann | 2011-02-10 10:20:51 -0800 (Thu, 10 Feb 2011) | 1 line

Bugfixes relating to collision energy

r5304 | pcbrefugee | 2011-02-05 23:29:58 -0800 (Sat, 05 Feb 2011) | 1 line

[PepC] fix a bug in build when ant is present

r5303 | slagelwa | 2011-02-02 14:20:00 -0800 (Wed, 02 Feb 2011) | 2 lines

Adding some default parameter file templates for the Q commands

r5302 | slagelwa | 2011-02-02 14:17:20 -0800 (Wed, 02 Feb 2011) | 7 lines

  • Updated submission interface
  • Now checks for write permissions on database file directory as myrimatch 
 can/will write a *.fasta.index file if it doesn't exist
  • Quoted a lot of the shell variables in the vain attempt to support 
 filenames with spaces in them


r5301 | slagelwa | 2011-02-02 14:01:03 -0800 (Wed, 02 Feb 2011) | 2 lines

update paths/queue name

r5300 | slagelwa | 2011-02-02 14:00:09 -0800 (Wed, 02 Feb 2011) | 2 lines

Beta version which submits jobs to a PBS cluster

r5299 | mhoopmann | 2011-02-01 15:28:43 -0800 (Tue, 01 Feb 2011) | 1 line

Better handling of bogus file names.

r5298 | mhoopmann | 2011-01-31 11:46:30 -0800 (Mon, 31 Jan 2011) | 1 line

removing mzParser from VPATH

r5297 | mhoopmann | 2011-01-31 11:10:01 -0800 (Mon, 31 Jan 2011) | 1 line

bugfixes

r5296 | real_procopio | 2011-01-28 15:40:48 -0800 (Fri, 28 Jan 2011) | 1 line

Upgrading to revision r25 of Lorikeet

r5295 | mhoopmann | 2011-01-28 11:15:35 -0800 (Fri, 28 Jan 2011) | 8 lines

builds mzParser now




...(hopefully)

r5294 | mhoopmann | 2011-01-28 11:01:38 -0800 (Fri, 28 Jan 2011) | 5 lines

Creating mzParser, an alternative to ramp. It reads mzXML and mzML without ProteoWizard (ie fast mzML reading). Includes ramp interface so that the transition is to replace the ramp.h with mzParser.h. Requires expat and zlib. To use: 1. compile mzParser.lib (libmzparser.a on linux). 2. in your source, include mzParser.h 3. link to mzParser.lib, expat.lib, zlib.lib

r5293 | real_procopio | 2011-01-26 17:33:53 -0800 (Wed, 26 Jan 2011) | 1 line

[bug] Rolling back incorrect commit!

r5292 | real_procopio | 2011-01-26 17:27:40 -0800 (Wed, 26 Jan 2011) | 1 line

Lorikeet resources: css, images, and js code

r5291 | real_procopio | 2011-01-26 17:27:27 -0800 (Wed, 26 Jan 2011) | 1 line

Lorikeet resources: css, images, and js code

r5290 | pcbrefugee | 2011-01-25 17:33:33 -0800 (Tue, 25 Jan 2011) | 1 line

[Tandem2XML] integrate Brendan's fix for handling fragment mass type "average", also use our standard filename handling to correct recent change that was case sensitive and not future-proof.

r5289 | pcbrefugee | 2011-01-18 16:38:58 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] object serialization for hadoop work

r5288 | pcbrefugee | 2011-01-18 14:58:17 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] tweak for less noisy download of tandem binary from AWS S3

r5287 | pcbrefugee | 2011-01-18 14:53:24 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem] add newline at end of file for quiet compile

r5286 | pcbrefugee | 2011-01-18 14:51:58 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] tweaks for quiet compile

r5285 | pcbrefugee | 2011-01-14 10:49:25 -0800 (Fri, 14 Jan 2011) | 1 line

[pwiz] synch up with official code rev 2465. (note: I also merged the local changes in our rev 5279 back to the official pwiz codebase, so we're fully synched)

r5284 | mhoopmann | 2011-01-13 15:00:18 -0800 (Thu, 13 Jan 2011) | 1 line

Detangled mscore_hrk and mscore_k class extensions. mscore_hrk now directly extends mscore.

r5283 | pcbrefugee | 2011-01-12 12:11:18 -0800 (Wed, 12 Jan 2011) | 1 line

[xtandem - hadoop] - don't depend on presence of sed on hadoop nodes to tidy up path names in final result file (more efficient to do it in memory before writing the file, anyway)

r5282 | pcbrefugee | 2011-01-07 19:26:17 -0800 (Fri, 07 Jan 2011) | 1 line

[xtandem] support for hadoop clusters that aren't hosted by Amazon Web Services. Horribly, this involves cygwin if you want to run it on Windows.

r5281 | real_procopio | 2011-01-04 15:10:22 -0800 (Tue, 04 Jan 2011) | 1 line

[Tandem2XML] Add support for z,c,a,x ion series; report correct number of potential peaks based on ion series used in search

r5280 | real_procopio | 2011-01-04 10:01:08 -0800 (Tue, 04 Jan 2011) | 1 line

Set the permissions on the png files (was a copy/paste error)

r5279 | dshteyn | 2011-01-03 16:11:00 -0800 (Mon, 03 Jan 2011) | 1 line

Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.

r5278 | real_procopio | 2011-01-03 11:07:30 -0800 (Mon, 03 Jan 2011) | 1 line

Corrected path to src root

r5277 | real_procopio | 2010-12-30 17:14:37 -0800 (Thu, 30 Dec 2010) | 1 line

Adding Lorikeet viewer to Windows installer

r5276 | real_procopio | 2010-12-30 17:13:58 -0800 (Thu, 30 Dec 2010) | 1 line

Adding Lorikeet viewer to Makefile

r5275 | real_procopio | 2010-12-30 17:12:24 -0800 (Thu, 30 Dec 2010) | 1 line

Adding Lorikeet viewer

r5274 | pcbrefugee | 2010-12-27 16:14:15 -0800 (Mon, 27 Dec 2010) | 1 line

htmldoc config doesn't handle MinGW, don't attempt to build it there

r5273 | pcbrefugee | 2010-12-27 15:46:31 -0800 (Mon, 27 Dec 2010) | 1 line

[Sqt2XML] include stdlib.h for best portability (some compilers weren't finding atoi(), etc)

r5272 | pcbrefugee | 2010-12-27 15:45:09 -0800 (Mon, 27 Dec 2010) | 1 line

cast for quiet compile

r5271 | pcbrefugee | 2010-12-27 15:38:42 -0800 (Mon, 27 Dec 2010) | 1 line

[InterProphetParser] add a couple of new files to MSVC InterProphetParser build files

r5270 | pcbrefugee | 2010-12-27 15:08:34 -0800 (Mon, 27 Dec 2010) | 1 line

C++ standard (or at least, older, portable revs of the standard) doesn't allow a ctor to call another variant of itself. But we can use default parameter values instead to achieve the same effect.

r5269 | pcbrefugee | 2010-12-27 14:21:35 -0800 (Mon, 27 Dec 2010) | 1 line

[mzXML2Search] add a couple of signed/unsigned casts for quiet compile

r5268 | pcbrefugee | 2010-12-27 13:24:06 -0800 (Mon, 27 Dec 2010) | 1 line

[owiz] sigh, and couple more missed adds, probably not the last

r5267 | pcbrefugee | 2010-12-27 13:18:21 -0800 (Mon, 27 Dec 2010) | 1 line

[pwiz] missed a couple of adds

r5266 | pcbrefugee | 2010-12-27 13:02:26 -0800 (Mon, 27 Dec 2010) | 1 line

Get current with ProteoWizard (SVN 2435) in anticipation of mzML read performance enhancements. Note you'll probably need to do a "make clean-pwiz pwiz".

r5265 | pcbrefugee | 2010-12-23 13:43:22 -0800 (Thu, 23 Dec 2010) | 1 line

revert to previous version - last committed code cannot be built. Missing comma in initializer list, references to class members not declared in class header, kind of a mess.

r5264 | dshteyn | 2010-12-23 10:43:24 -0800 (Thu, 23 Dec 2010) | 1 line

Filter out extension from Tandem spectrum names.

r5263 | pcbrefugee | 2010-12-22 15:36:55 -0800 (Wed, 22 Dec 2010) | 1 line

[xtandem] add ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds.

r5262 | pcbrefugee | 2010-12-22 15:34:46 -0800 (Wed, 22 Dec 2010) | 1 line

[xtandem] a couple more ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds.

r5261 | pcbrefugee | 2010-12-22 15:15:49 -0800 (Wed, 22 Dec 2010) | 2 lines

[xtandem] add ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds. Also add the new scoring functions to the MSVC builds.

r5260 | pcbrefugee | 2010-12-22 15:10:07 -0800 (Wed, 22 Dec 2010) | 1 line

add some explicit double->float casts for quiet compile

r5259 | mhoopmann | 2010-12-22 14:48:13 -0800 (Wed, 22 Dec 2010) | 1 line

bugfix relating to hrK-score

r5258 | pcbrefugee | 2010-12-22 13:37:27 -0800 (Wed, 22 Dec 2010) | 1 line

[tandem native mzML reader] - completely untested changes to enable reading of zlib-compressed peaks in mzML, for Joe's perusal (nothing else in this directory is expected to work yet either so I don't feel bad).

r5257 | mhoopmann | 2010-12-22 12:42:28 -0800 (Wed, 22 Dec 2010) | 1 line

Added two new scoring functions, and expanded virtual function declarations in mscore.h to allow more functions to be overloaded in the pluggable algorithms. Also changed A-ions to use A-dot.

r5256 | pcbrefugee | 2010-12-20 13:04:38 -0800 (Mon, 20 Dec 2010) | 16 lines

[xtandem - defork work] Adding a couple of directories for inspection by other developers - these are *not* part of the build.

src_merged - this is my proposed but INCOMPLETE merge of current (12/1/2010) official X!Tandem code with our current src directory, as of SVN rev 5252 (so it includes my Hadoop work). It should compile just fine but I've not tried to run any data through it yet - there are questions to be answered first.

src_cyclone - this is unaltered code from the 12/1/2010 release of X!Tandem, for comparison purposes, don't edit this, and don't expect it to compile.


RISKS

This is a long delayed update of a forked project, and I worry about possibly having tossed out changes made from the ISB/LabKey/Insilicos camp but not commented as such. Somebody other than and in addition to me should do a careful before-and-after comparison across the whole directory.

The mscore area is of greatest concern - my sense is that there are substantial changes needed to the k score because there are substantial changes to the standard tandem scoring function since our last synch-up. Do a 3-way diff src_merged, src_cyclone, and src to get a feel for the changes. The src_cyclone code really punted on this one with an ifdef for pluggable scoring that, to my eye, screams "you are falling behind". I do wonder though how much of the new work really belongs in the mscore class instead of the mscore_tandem child class it's in now.

We should look hard at replacing the pwiz code with the new mzML read code, although I've not really given it the once over. Probably doesn't do compressed peaklists at the moment if its consistent with the tandem mzXML read code.

There's a fair bit of customization on our side in mspectrumcondition.cpp, around max mass and max charge. It looks to me like the official code is buggy, I put an email in. Ron's response is that yes, a lot of that is cruft. I've offered him a patch including the max mass filter.

r5255 | ppatrick | 2010-12-20 07:57:57 -0800 (Mon, 20 Dec 2010) | 1 line

Fixed bug in parsing filterLine containing sa (supplemental activation) param. [MS2 scans with sa where being converted as msLevel=0]

r5254 | pcbrefugee | 2010-12-17 09:06:33 -0800 (Fri, 17 Dec 2010) | 1 line

[general XML file handling] add a retry loop to the overwrite routine's success checker to accomodate slow file systems (such as network shares)

r5253 | pcbrefugee | 2010-12-17 09:03:38 -0800 (Fri, 17 Dec 2010) | 1 line

[SpecraST] a couple of int/unsigned casts for quiet compile

r5252 | pcbrefugee | 2010-12-15 14:43:15 -0800 (Wed, 15 Dec 2010) | 1 line

[xtandem/hadoop] - tidier exit on success

r5251 | pcbrefugee | 2010-12-15 13:00:34 -0800 (Wed, 15 Dec 2010) | 1 line

[MSVC build] add a little build-time message explaining the need for MinGW even when using MSVC, and pointing the developer at the README_WIN.txt file

r5250 | slagelwa | 2010-12-13 16:38:52 -0800 (Mon, 13 Dec 2010) | 2 lines

Removing defunct branch to build TPP under Visual Studio 2008 Express

r5249 | dshteyn | 2010-12-13 11:47:54 -0800 (Mon, 13 Dec 2010) | 1 line

Fix bug with output of precursor_intensity.

r5248 | pcbrefugee | 2010-12-13 10:32:29 -0800 (Mon, 13 Dec 2010) | 1 line

[xtandem] fix the linux "make install" target that I broke when I changed the build artifact for linux from "tandem.exe" to just "tandem"

r5247 | pcbrefugee | 2010-12-10 17:06:33 -0800 (Fri, 10 Dec 2010) | 1 line

[xtandem+hadoop] move the code that identifies machine type into its own script for use by bundler and installers alike

r5246 | dshteyn | 2010-12-10 16:26:41 -0800 (Fri, 10 Dec 2010) | 1 line

iModelParser.cgi: fix bugs with getting page to display. Now displays but the overlapping colors of gnuplot don't work. For best results use gnuplot 4.4

r5245 | pcbrefugee | 2010-12-10 15:29:23 -0800 (Fri, 10 Dec 2010) | 1 line

[xtandem+hadoop] a script for building xtandem (and x!!tandem if possible) and publishing to S3 for use in EC2 or other clusters via wget

r5244 | pcbrefugee | 2010-12-10 15:27:40 -0800 (Fri, 10 Dec 2010) | 1 line

[EC2 build] warn rather than fail when CentOS version is identified as other than 5.2

r5243 | pcbrefugee | 2010-12-10 14:14:54 -0800 (Fri, 10 Dec 2010) | 1 line

quiet a "no newline at end of file" warning

r5242 | dshteyn | 2010-12-10 00:26:53 -0800 (Fri, 10 Dec 2010) | 1 line

PepXMLViewer: adding collision_energy, precursor_intensity and compensation_voltage

r5241 | dshteyn | 2010-12-10 00:18:05 -0800 (Fri, 10 Dec 2010) | 1 line

PepXMLViewer: support for Crux

r5240 | dshteyn | 2010-12-10 00:16:24 -0800 (Fri, 10 Dec 2010) | 1 line

InteractParser,xinteract: new feature precursor intensity in pepXML

r5239 | pcbrefugee | 2010-12-09 17:35:41 -0800 (Thu, 09 Dec 2010) | 1 line

[xtandem] - extending the TPP fork of X!Tandem to optionally encompass the X!!Tandem MPI capability (make target "bbtandem", needs MPICH2 devkit) and to operate under MapReduce when used with special commandline arguments (see xtandem_mapreduce.py invocation script). Currently targeted at Amazon Web Services Elastic MapReduce service but work is ongoing to make it useful on straight-up Hadoop clusters (that is, without the amazon API frontending it). Not fabulously well documented yet, but have a look at README-MAPREDUCE for some details.

r5238 | dshteyn | 2010-12-09 10:50:09 -0800 (Thu, 09 Dec 2010) | 1 line

RAMP: adding parsing of compensationVoltage (FAIMS).

r5237 | dshteyn | 2010-12-08 11:23:30 -0800 (Wed, 08 Dec 2010) | 1 line

pepXML schema update for collision_energy and compensation_voltage

r5236 | dshteyn | 2010-12-08 11:18:18 -0800 (Wed, 08 Dec 2010) | 1 line

xinteract: New features, report collision energy, report compensation voltage

r5235 | dshteyn | 2010-12-08 11:08:18 -0800 (Wed, 08 Dec 2010) | 1 line

InteractParser: New features, report collision energy, report compensation voltage, fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max rank option to not report hits above a certain hit_rank.

r5234 | dshteyn | 2010-12-07 15:27:09 -0800 (Tue, 07 Dec 2010) | 1 line

Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query

r5233 | slagelwa | 2010-12-07 14:56:42 -0800 (Tue, 07 Dec 2010) | 4 lines

Added HCD and ETD+SA to the activationMethod attribute Added compensationVoltage to the scan element


r5232 | slagelwa | 2010-12-07 11:13:10 -0800 (Tue, 07 Dec 2010) | 8 lines

Adding mzXML 3.1 version. This file was obtained from:

http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_3.1.xsd.

I'm presuming that this is the correct file, and that this is the correct location in subversion for these files.


r5231 | real_procopio | 2010-12-02 15:06:33 -0800 (Thu, 02 Dec 2010) | 1 line

New NIGMS imagem -- with thick border!

r5230 | real_procopio | 2010-12-02 15:03:51 -0800 (Thu, 02 Dec 2010) | 1 line

Use new NIGMS image instead of NHLBI

r5229 | real_procopio | 2010-12-02 14:55:06 -0800 (Thu, 02 Dec 2010) | 4 lines

[Petunia] Added mouse-over tooltips for menu items and navigation tabs; Added NIGMS logo and credits; replacing NHLBI's

r5228 | real_procopio | 2010-12-02 14:53:29 -0800 (Thu, 02 Dec 2010) | 1 line

New NIGMS image

r5227 | real_procopio | 2010-12-01 17:11:04 -0800 (Wed, 01 Dec 2010) | 5 lines

[Petunia] Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation; Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support; Minor bug fix when file is not present (as opposed to unreadable).

r5226 | slagelwa | 2010-12-01 17:03:18 -0800 (Wed, 01 Dec 2010) | 2 lines

Added inspect.params templates and checkin in omssa, tandem, README

r5225 | real_procopio | 2010-11-30 14:36:01 -0800 (Tue, 30 Nov 2010) | 11 lines

Adjusted Xpress defaults; Centralized code that creates links to open files in respective viewers; Fixed broken Set Working Dir feature, also fixed link when output is a directory; Added direct access to switch a directory in File Browser; Moved "timeout" link to the right to avoid overlap with update page link; Added confirmation message when switching pipeline type; Shortened some menu titles to save space; Updated meaning of $in_windows and introduced $in_cygwin vars; Removed some seemingly unused code; Small code formatting/alignment changes.

r5224 | real_procopio | 2010-11-30 14:33:42 -0800 (Tue, 30 Nov 2010) | 1 line

Menus are now semi-transparent in Chrome

r5223 | pcbrefugee | 2010-11-23 15:43:28 -0800 (Tue, 23 Nov 2010) | 1 line

[build] default to Ubuntu 9_x on AWS is Ubuntu distro isn't recognised (because it's Ubuntu 10-something, probably, but try 9_x tool set since it probably works fine)

r5222 | henrylam | 2010-11-17 20:13:36 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Shorten peak annotation to save memory during search

r5221 | henrylam | 2010-11-17 20:05:28 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Add massdiff information to library. Option to exclude IDs of too big massdiff.

r5220 | henrylam | 2010-11-17 19:57:47 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Add headers to xls and txt search output. No-header format can still be had with -sEnxls and -sEntxt options

r5219 | slagelwa | 2010-11-15 16:07:38 -0800 (Mon, 15 Nov 2010) | 2 lines

Added ability to upload files to a working directory. Very useful if you happen to be running TPP on the cloud.

r5218 | eng_jk | 2010-11-10 19:30:25 -0800 (Wed, 10 Nov 2010) | 2 lines

set ms2 format retention time to minutes

r5217 | dshteyn | 2010-11-10 15:52:17 -0800 (Wed, 10 Nov 2010) | 1 line

Fix parsing of Phenyx search results.

r5216 | dshteyn | 2010-10-29 16:23:37 -0700 (Fri, 29 Oct 2010) | 1 line

make SearchHit separate class for iProphet.

r5215 | dshteyn | 2010-10-29 16:18:35 -0700 (Fri, 29 Oct 2010) | 1 line

Clear out tophit hashes before recomputing. Separate SearchHit in a different class.

r5214 | slagelwa | 2010-10-25 10:20:36 -0700 (Mon, 25 Oct 2010) | 1 line

[4.4.1 release] tagging release from branch

r5213 | henrylam | 2010-10-22 02:49:33 -0700 (Fri, 22 Oct 2010) | 1 line

[SpectraST] Similarity clustering feature -- work in progress

r5212 | henrylam | 2010-10-22 02:34:59 -0700 (Fri, 22 Oct 2010) | 1 line

[SpectraST] Partial revert to old insertForSearch behavior to keep search results invariant

r5211 | henrylam | 2010-10-20 21:24:03 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Add feature: ProbTable (-cT option) can retrieve entries of any charge by leaving out the /<charge> in the table

r5210 | henrylam | 2010-10-20 21:14:02 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Add option to record all raw spectra going into a consensus; RawSpectrum/RawSpectra field now excludes .charge

r5209 | henrylam | 2010-10-20 20:23:39 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Fix bug with rarely used spectrum plotting feature; clean up SpectraSTReplicates flow

r5208 | eng_jk | 2010-10-20 15:34:46 -0700 (Wed, 20 Oct 2010) | 3 lines

noticed crazy scan numbers in an mzXML file (agilent .d via msconvert); this small change keeps status output behaving as intended for the crazy scan #s

r5207 | henrylam | 2010-10-19 03:31:40 -0700 (Tue, 19 Oct 2010) | 1 line

[SpectraST] For faster search, more economical insert() in SpectraSTPeakList

r5206 | eng_jk | 2010-10-18 15:20:01 -0700 (Mon, 18 Oct 2010) | 2 lines

simply change from double to single space as separating char

r5205 | dshteyn | 2010-10-18 10:45:43 -0700 (Mon, 18 Oct 2010) | 1 line

Use | as another separator for getting the protein name

r5204 | henrylam | 2010-10-18 03:07:07 -0700 (Mon, 18 Oct 2010) | 1 line

[SpectraST] Enable several new ways of retrieving entries from SpectraSTMzLibIndex: delayed read, sort by s/n

r5203 | henrylam | 2010-10-18 03:01:07 -0700 (Mon, 18 Oct 2010) | 1 line

[SpectraST] Add (hidden) option of limiting number of peaks of library spectrum used in searching

r5202 | henrylam | 2010-10-18 01:00:42 -0700 (Mon, 18 Oct 2010) | 1 line

[MzXML2Search] Change interpretation of -A option when the scan has no activationMethod field in the mzXML file

r5201 | henrylam | 2010-10-18 00:35:16 -0700 (Mon, 18 Oct 2010) | 1 line

[ramp] Parse activationMethod in <scan> element -- msconvert put it there, not in <precursorMz>

r5200 | pcbrefugee | 2010-10-14 11:47:28 -0700 (Thu, 14 Oct 2010) | 1 line

[documentation] update the windows build notes to reflect the fact that one needs MinGW to configure certain libraries before MSVC can be used for building TPP

r5199 | dctrud | 2010-10-14 01:50:34 -0700 (Thu, 14 Oct 2010) | 1 line

[ASAPRatioProteinRatioParser] Removing cacheing changes from r4884 as can cause crashes on some input due to out of memory

r5198 | dshteyn | 2010-10-12 10:35:08 -0700 (Tue, 12 Oct 2010) | 1 line

Back out unfinished parts that broke the build.

r5197 | dshteyn | 2010-10-12 10:32:05 -0700 (Tue, 12 Oct 2010) | 1 line

Backing out system specific checkin that shouldn't've been, retaining the CLEVEL stuff

r5196 | pcbrefugee | 2010-10-12 09:37:03 -0700 (Tue, 12 Oct 2010) | 1 line

[xtandem] fixed a bug that caused all groups in the output file to have identical "sumI" and "maxI" intensity values when configured with "spectrum, use conditioning"="no". Also submitted a patch to the official X!Tandem project.

r5195 | dshteyn | 2010-10-11 17:28:27 -0700 (Mon, 11 Oct 2010) | 1 line

Petunia: Add feature for setting CLEVEL parameter on Analyze Peptides page

r5194 | dshteyn | 2010-10-11 17:25:24 -0700 (Mon, 11 Oct 2010) | 1 line

Fix option parsing bug

r5193 | dshteyn | 2010-10-11 17:23:20 -0700 (Mon, 11 Oct 2010) | 1 line

Fix options parsing bug

r5192 | slagelwa | 2010-10-07 10:46:46 -0700 (Thu, 07 Oct 2010) | 2 lines

Remove debugging echo and don't delete mzML/mzXML files before conversion

r5191 | slagelwa | 2010-10-06 15:40:13 -0700 (Wed, 06 Oct 2010) | 2 lines

Fix nonzero exit status

r5190 | slagelwa | 2010-10-06 14:54:38 -0700 (Wed, 06 Oct 2010) | 2 lines

Fix silly cut&paste error

r5189 | slagelwa | 2010-10-06 14:34:35 -0700 (Wed, 06 Oct 2010) | 2 lines

New "qmascot" script for testing...

r5188 | slagelwa | 2010-10-06 14:34:06 -0700 (Wed, 06 Oct 2010) | 3 lines

Fixed default name of qgrid log file to ".log"


r5187 | slagelwa | 2010-10-06 14:31:18 -0700 (Wed, 06 Oct 2010) | 3 lines

Updated documentation on search programs, fixed copy problem in qinspect, and updated qconvert documentation.

r5186 | slagelwa | 2010-10-05 13:19:00 -0700 (Tue, 05 Oct 2010) | 2 lines

Quote remoteconvert (a.k.a msconvert) values to command flags

r5185 | slagelwa | 2010-09-29 15:23:50 -0700 (Wed, 29 Sep 2010) | 2 lines

4.4.1 fixes, including installer changes on perl, missing msconvert files, SpectraST fixes by Henry and fixes by Jimmy

r5184 | pcbrefugee | 2010-09-24 14:31:23 -0700 (Fri, 24 Sep 2010) | 5 lines

tweaks for building on Debian, which is the basis of the Amazon Elastic Map Reduce service recognize Debian 5.0.3, fall through to Ununtu 8 handling for that S3Fuse cache in /mnt instead of /mnt - less likely to fill the local volume don't use sudo if you're already root (normally harmless except that debian hasn't got sudo and you're already root anyway)

r5183 | slagelwa | 2010-09-24 10:04:37 -0700 (Fri, 24 Sep 2010) | 2 lines

Cleaned up convert comments, fixed newline issue with omssa parameters

r5182 | rbs66 | 2010-09-22 14:47:10 -0700 (Wed, 22 Sep 2010) | 1 line

Added full path to rm command.

r5181 | slagelwa | 2010-09-21 10:35:54 -0700 (Tue, 21 Sep 2010) | 2 lines

Fixing placement of '@' in htmldoc make command

r5180 | dshteyn | 2010-09-20 16:30:19 -0700 (Mon, 20 Sep 2010) | 1 line

no autoconf

r5179 | dshteyn | 2010-09-20 16:18:07 -0700 (Mon, 20 Sep 2010) | 1 line

htmldoc added for export to pdf

r5178 | dshteyn | 2010-09-20 16:16:53 -0700 (Mon, 20 Sep 2010) | 1 line

htmldoc added for export to pdf

r5177 | eng_jk | 2010-09-20 16:05:10 -0700 (Mon, 20 Sep 2010) | 2 lines

add check to the initialization function to avoid possible negative index value

r5176 | eng_jk | 2010-09-20 16:03:20 -0700 (Mon, 20 Sep 2010) | 2 lines

add check to the initialization function to avoid possible negative index value

r5175 | pcbrefugee | 2010-09-14 17:37:49 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] oops, hit the wrong header file in last commit

r5174 | pcbrefugee | 2010-09-14 17:34:12 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] destructor was deleting a string it hadn't allocated

r5173 | pcbrefugee | 2010-09-14 17:27:13 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] remove redundant iModelParser:: within iModelParser class declaration

r5172 | pcbrefugee | 2010-09-14 17:26:26 -0700 (Tue, 14 Sep 2010) | 1 line

[ModelParser] fix memory leak

r5171 | pcbrefugee | 2010-09-14 17:03:10 -0700 (Tue, 14 Sep 2010) | 1 line

tweak my previous tweak. Crossplatform is hard!

r5170 | pcbrefugee | 2010-09-14 16:30:50 -0700 (Tue, 14 Sep 2010) | 1 line

[RTCalculator] add missing function return values that could cause some mysterious behavior, also add various casts and more widely portable dynamic allocations to make more compilers happy

r5169 | eng_jk | 2010-09-14 16:06:20 -0700 (Tue, 14 Sep 2010) | 2 lines

fix previous check-in

r5168 | dshteyn | 2010-09-14 16:02:08 -0700 (Tue, 14 Sep 2010) | 1 line

Fix compilation issues with iModelParser.cgi tool.

r5167 | eng_jk | 2010-09-14 11:55:39 -0700 (Tue, 14 Sep 2010) | 2 lines

add 5158 fix to trunk

r5166 | eng_jk | 2010-09-14 09:38:50 -0700 (Tue, 14 Sep 2010) | 4 lines

same single readIndex call from commit 5160 going to trunk update accurate fragment ion calculations remove unused pepnovo code

r5165 | dshteyn | 2010-09-13 17:17:49 -0700 (Mon, 13 Sep 2010) | 1 line

Fix compilation problem and logic for detecting obs_charge_distr reported by Natalie

r5164 | rbs66 | 2010-09-10 16:52:39 -0700 (Fri, 10 Sep 2010) | 1 line

Removed duplicate line from last update.

r5163 | rbs66 | 2010-09-10 16:28:26 -0700 (Fri, 10 Sep 2010) | 1 line

Updated to display iProb links in Petunia that lead to analysis results for iProphet pep xml files.

r5162 | rbs66 | 2010-09-10 16:23:18 -0700 (Fri, 10 Sep 2010) | 1 line

Added commands for iModelParser.cgi, the iProphet pep xml viewer in Petunia.

r5161 | rbs66 | 2010-09-10 16:18:56 -0700 (Fri, 10 Sep 2010) | 1 line

Added updates to RTCalc in Petunia including retention time training page.

r5160 | eng_jk | 2010-09-10 15:35:12 -0700 (Fri, 10 Sep 2010) | 2 lines

issue readIndex call once and use for both ms/ms and ms1 plots

r5159 | pcbrefugee | 2010-09-10 13:56:18 -0700 (Fri, 10 Sep 2010) | 1 line

[pwiz, ramp, plot-msms.cgi] update RAMP to use new pwiz RAMPAdapter functionality for more efficient scan number lookups, for performance boost in plot-msms CGI

r5158 | eng_jk | 2010-09-10 12:09:13 -0700 (Fri, 10 Sep 2010) | 5 lines

Fix error of an array not being initialized (line 2910) presumably introduced in last bugfix checkin. Effect was a bunch of peptides not being quantified; surprised it even produced results at all.


r5157 | dshteyn | 2010-09-09 11:36:51 -0700 (Thu, 09 Sep 2010) | 1 line

Implementing additional functions for peptide parameters borrowed from Elude. Output file option. Cleanup of ANN specification (now done using 1 file).

r5156 | pcbrefugee | 2010-09-03 10:16:32 -0700 (Fri, 03 Sep 2010) | 1 line

change a statically allocated buffer to dynamic - could cause problems with stack-allocated ogzstream

r5155 | dshteyn | 2010-09-02 11:29:23 -0700 (Thu, 02 Sep 2010) | 1 line

Use one file to reference all neural net stuff.

r5154 | dshteyn | 2010-09-02 09:57:16 -0700 (Thu, 02 Sep 2010) | 1 line

New peptide features based on Elude model. Capture neural network parameter index in a separate file.

r5153 | slagelwa | 2010-09-01 14:35:32 -0700 (Wed, 01 Sep 2010) | 2 lines

  • Perl check now presents a "abort/retry/ignore" dialog if the perl check fails -- allowing users to continue the installation in the event this a failed perl check...fails
  • Remove annoying "\" in the main window dialog. I shouldn't do this but...

r5152 | slagelwa | 2010-09-01 14:32:41 -0700 (Wed, 01 Sep 2010) | 1 line

Fix perl 5.12 test. Added comment about a cleaner way to do the test, but did not make the change.

r5151 | rbs66 | 2010-08-30 17:06:15 -0700 (Mon, 30 Aug 2010) | 1 line

Added backwards compatibility with older pep xml file versions.

r5150 | rbs66 | 2010-08-30 17:03:50 -0700 (Mon, 30 Aug 2010) | 1 line

CHanged to work with new modified util functions.

r5149 | rbs66 | 2010-08-30 17:02:54 -0700 (Mon, 30 Aug 2010) | 1 line

Updated xml schema to 116.

r5148 | rbs66 | 2010-08-30 17:01:06 -0700 (Mon, 30 Aug 2010) | 1 line

Added tags for Model Parser updated to schema.

r5147 | slagelwa | 2010-08-30 13:48:52 -0700 (Mon, 30 Aug 2010) | 2 lines

Fixing SVN add issue

r5146 | henrylam | 2010-08-29 20:49:31 -0700 (Sun, 29 Aug 2010) | 1 line

[SpectraST] Updated XREA calculation

r5145 | henrylam | 2010-08-29 20:14:43 -0700 (Sun, 29 Aug 2010) | 1 line

[SpectraST] Fix re-annotation crash; ensure m/z order of peak list; minor stylistic changes

r5144 | pcbrefugee | 2010-08-27 17:26:23 -0700 (Fri, 27 Aug 2010) | 1 line

this stops the unneeded fann/gsl rebuilds my last change caused on the linux side

r5143 | pcbrefugee | 2010-08-27 16:44:15 -0700 (Fri, 27 Aug 2010) | 1 line

don't try to run ant if it's not installed

r5142 | pcbrefugee | 2010-08-27 15:59:36 -0700 (Fri, 27 Aug 2010) | 1 line

clear up potential malloc/free/new/delete confusion by refactoring some path manipulation routines in util.h to return std::string instead

r5141 | pcbrefugee | 2010-08-27 14:37:40 -0700 (Fri, 27 Aug 2010) | 1 line

build the FANN and GSL libs even if the directory already exists (as when MSVC build is performed before MinGW build)

r5140 | pcbrefugee | 2010-08-27 14:10:30 -0700 (Fri, 27 Aug 2010) | 1 line

[ModelParser] GCC 4 wouldn't compile "sprintf(tmp, tag->getAttributeValue(tmp));" due to "error: format not a string literal and no format arguments". Upon inspection there's a memory leak as well as a potential crash from naively using the possibly NULL result of tag->getAttributeValue(), and a probable buffer overrun as well, I cleaned these up.

r5139 | pcbrefugee | 2010-08-27 12:13:45 -0700 (Fri, 27 Aug 2010) | 1 line

deal with a strict GCC 4 warning for failure to check fgets return value

r5138 | rbs66 | 2010-08-27 10:48:03 -0700 (Fri, 27 Aug 2010) | 1 line

Fixed function call where string length was passed instead of its entire possible size. Deleted a couple comments.

r5137 | rbs66 | 2010-08-26 16:36:59 -0700 (Thu, 26 Aug 2010) | 1 line

Quick recommit to fix minor Java bug with charge tab selection.

r5136 | rbs66 | 2010-08-26 16:15:22 -0700 (Thu, 26 Aug 2010) | 1 line

Fixed some minor memory problems and tricky incorrect file path bug.

r5135 | slagelwa | 2010-08-26 15:44:38 -0700 (Thu, 26 Aug 2010) | 3 lines

Use -terse when on the sun grid engine to mimic output functionality that happens in PBS

r5134 | pcbrefugee | 2010-08-26 14:27:32 -0700 (Thu, 26 Aug 2010) | 1 line

add Crux support to MSVC builds

r5133 | pcbrefugee | 2010-08-26 13:59:46 -0700 (Thu, 26 Aug 2010) | 2 lines

remove useless null pointer checks before free and delete (free and delete handle NULL just fine, this just slows down some very heavily used code) remove useless nulling of pointers in destructors (worse than useless, actually - potentially hides double-free problems in calling code)

r5132 | rbs66 | 2010-08-25 15:41:42 -0700 (Wed, 25 Aug 2010) | 1 line

Recommitting changes that had problems merging.

r5131 | rbs66 | 2010-08-25 15:34:26 -0700 (Wed, 25 Aug 2010) | 2 lines

Recommitted due to problems merging. Originally updated to write roc curve data and error data for individual charges, for use with Model Parser updates.

r5130 | dshteyn | 2010-08-25 15:33:53 -0700 (Wed, 25 Aug 2010) | 1 line

Safer Array freeing

r5129 | dshteyn | 2010-08-25 15:32:44 -0700 (Wed, 25 Aug 2010) | 1 line

Make scan parsing from Mascot case insensitive

r5128 | dshteyn | 2010-08-25 15:31:21 -0700 (Wed, 25 Aug 2010) | 1 line

Crux support

r5127 | dshteyn | 2010-08-25 15:30:29 -0700 (Wed, 25 Aug 2010) | 1 line

Crux support

r5126 | dshteyn | 2010-08-25 15:29:41 -0700 (Wed, 25 Aug 2010) | 1 line

Support for Crux

r5125 | dshteyn | 2010-08-25 15:26:49 -0700 (Wed, 25 Aug 2010) | 1 line

Use CLEVEL in crux too

r5124 | slagelwa | 2010-08-25 15:04:31 -0700 (Wed, 25 Aug 2010) | 2 lines

[merge 4.4] Merging head of 4.4 branch back into trunk

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